4TS2

Crystal structure of the Spinach RNA aptamer in complex with DFHBI, magnesium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.884 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein.

Warner, K.D.Chen, M.C.Song, W.Strack, R.L.Thorn, A.Jaffrey, S.R.Ferre-D'Amare, A.R.

(2014) Nat.Struct.Mol.Biol. 21: 658-663

  • DOI: 10.1038/nsmb.2865
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to l ...

    GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs.


    Organizational Affiliation

    Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Spinach aptamer RNA, bimolecular constructX44synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
Spinach aptamer RNA, bimolecular constructY47synthetic construct
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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X, Y
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SUC
Query on SUC

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Y
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
CCC
Query on CCC

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Download CCD File 
Y
CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
C9 H13 N3 O10 P2
IZJNKZMLZILGRK-XVFCMESISA-N
 Ligand Interaction
38E
Query on 38E

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Download CCD File 
Y
(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one
C12 H10 F2 N2 O2
ZDDIJYXDUBFLID-YHYXMXQVSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
X, Y
RNA LINKINGC9 H13 N3 O10 P2C
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.884 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.877α = 90.00
b = 49.399β = 90.00
c = 188.410γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary